Design, synthesis, and molecular modeling studies of 5′-deoxy-5′-ureidoadenosine: 5′-ureido group as multiple hydrogen bonding donor in the active site of S-adenosylhomocysteine hydrolase

Article abstract of DOI:10.1016/j.bmcl.2007.06.013

5′-Deoxy-5′-ureidoadenosine was designed and synthesized as a potent inhibitor of S-adenosylhomocysteine hydrolase (SAH), in which 5′-ureido group acted as multiple hydrogen bonding donor in binding with active site residues of SAH in the molecular modeli

Full text of DOI:10.1016/j.bmcl.2007.06.013

Bioorganic & Medicinal Chemistry Letters 17 (2007) 4456–4459
Design, synthesis, and molecular modeling studies
of 50-deoxy-50-ureidoadenosine: 50-ureido group as
multiple hydrogen bonding donor in the active site
of S-adenosylhomocysteine hydrolase
Ting Wang,a,b Hyun Joo Lee,a Dilip K. Tosh,a Hea Ok Kim,a Shantanu Pal,a
Sun Choi,a Yoonji Lee,a Hyung Ryong Moon,c Long Xuan Zhao,a,b
Kang Man Leea,* and Lak Shin Jeonga,*
aLaboratory of Medicinal Chemistry, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
bCollege of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116-029, China
cCollege of Pharmacy, Pusan National University, Busan 609-753, Republic of Korea
Received 16 April 2007; revised 19 May 2007; accepted 2 June 2007
Available online 8 June 2007
Abstract—50-Deoxy-50-ureidoadenosine was designed and synthesized as a potent inhibitor of S-adenosylhomocysteine hydrolase
(SAH), in which 50-ureido group acted as multiple hydrogen bonding donor in binding with active site residues of SAH in the molec-
ular modeling study.
ꢀ 2007 Published by Elsevier Ltd.
S-Adenosylhomocysteine hydrolase (SAH) is an enzyme
catalyzing interconversion of S-adenosylhomocysteine
into adenosine and L-homocysteine.1–3 Inhibition of
this enzyme accumulates S-adenosylhomocysteine
intracellularly, resulting in feed-back inhibition of trans-
methylation by S-adenosylmethionine-dependent meth-
yltransferase.1–3 Since transmethylation is essential for
mRNA capping of most animal infecting viruses, SAH
has been a good therapeutic target for the development
of broad-spectrum antiviral agents.4,5
be capable of forming multiple hydrogen bonding. Here-
in, we report the synthesis, enzyme inhibitory activity,
and molecular modeling studies of 50-deoxy-50-ureido-
adenosine (3) (Fig. 1).
The key strategy to the synthesis of the desired nucleo-
sides 2 and 3 was the conversion of the 50-azido deriva-
tive to the 50-amino- and 50-ureido derivatives. Thus, we
first synthesized the 50-azido derivative, as shown in
Scheme 1.
Recently, we have reported the 50-amino derivative 1 of
fluoro-neplanocin A as a potent inhibitor of SAH, in
which 50-amino group acted as a good hydrogen bond-
ing donor in the active site of SAH.6 Thus, on the basis
of these findings, we first designed the 50-amino-50-deox-
yadenosine (2) and compared its SAH inhibitory activity
with that of 1. Then, in order to confirm the role of 50-
substituent as a hydrogen bonding donor in the active
site of SAH, we designed the 50-ureido derivative 3 to
Synthesis began with commercially available N6-ben-
zoyladenosine (4). Treatment of 4 with 2,2-dimethoxy-
propane and acetone in the presence of catalytic
amounts of sulfuric acid gave 2,3-isopropylidene deriva-
tive 5. Compound 5 was treated with mesyl chloride fol-
lowed by heating the resulting mesylate 6 with sodium
azide in DMF yielded the 50-azido derivative 7 in good
yield. Removal of the isopropylidene group of 7 with
aqueous trifluoroacetic acid gave diol 8, which was trea-
ted with sodium methoxide to give 50-azido-50-deoxya-
denosine (9).7 Reduction of 50-azido derivative 9 with
Lindlar’s catalyst afforded the 50-amino derivative 2.7,8
Keywords: S-Adenosylhomocysteine hydrolase; 50-Ureidoadenosine;
Multiple hydrogen bonding donor.
*
Corresponding authors. Tel.: +82 2 3277 3466; fax: +82 2 3277 2851
(L.S.J.); tel.: +82 2 3277 3041; fax: +82 2 3277 2851 (K.M.L.); e-mail
addresses: lakjeong@ewha.ac.kr; kmlee@ewha.ac.kr
Conversion of the 50-azido group to the 50-ureido group
is illustrated in Scheme 2. Catalytic hydrogenation of
0960-894X/$ - see front matter ꢀ 2007 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2007.06.013

T. Wang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4456–4459
4457
NH2
N
NH2
N
NH2
N
N
N
N
N
O
N
N
F
H2N
N
N
N
H2N
H2N
N
O
O
H
HO
OH
HO
OH
HO
OH
3
1
2
Figure 1. The rationale for the design of 50-deoxy-50-ureidoadenosine (3).
NHBz
NHBz
NHBz
N
N
N
N
N
N
N
N
N
a
b
N
MsO
N
O
HO
N
O
HO
O
77%
from 4
O
O
c
O
O
OH OH
6
4
5
83%
NHBz
NH2
N
NHBz
N
N
N
N
N
N
N
N
d
N
e
N3
O
N
N
N3
N3
O
O
68%
from 7
O
O
OH OH
OH OH
9
7
8
92%
f
NH2
N
N
N
N
H2N
O
OH OH
2
Scheme 1. Reagents and conditions: (a) 2,2-dimethoxypropane, acetone, H2SO4, rt, 30 min; (b) MsCl, pyridine, rt, 30 min; (c) NaN3, DMF, 60 ꢁC,
3 h; (d) 50% aq CF3CO2H, rt, 1 h; (e) NaOMe, MeOH, rt, 24 h; (f) Lindlar’s catalyst, rt, 15 h.
NHBz
NHBz
NHBz
N
N
O
O
N
N
N
N
N
N
N
N
N
N
Cl
a
HN HN
b
H2N
N3
O
O
O
O
O
O
O
O
O
11
10
7
58%
from 7
c
NH2
NH2
N
N
N
O
N
N
O
d
N
H2N HN
N
O
O
N
H2N HN
O
63%
O
OH OH
12
3
Scheme 2. Reagents and conditions: (a) H2, Pd/C, MeOH, rt, 24 h; (b) chloroacetyl isocyanate, DMF, 0 ꢁC, 4 h; (c) NaOMe, MeOH, rt, overnight;
(d) 50% aq CF3CO2H, rt, 1 h.

4458
T. Wang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4456–4459
Table 1. SAH inhibitory activity of the final nucleosides 2, 3, and 9
studies were performed with Surflex-Dock in SYBYL
7.3.3 (Tripos, Inc.) using a reported X-ray crystal struc-
ture of human SAH (i.e., 1LI4.pdb14).
NH2
N
N
Since X-ray co-crystal structure of human SAH with its
ligand, neplanocin A, showed that neplanocin A was in
its oxidized form at C30 position which was enzymati-
cally oxidized by the cofactor NAD+, the synthesized
ligands were modified to their oxidized forms and
docked into SAH with the cofactor in its reduced, form
NADH. The 50-hydroxyl group of the original co-crys-
tallized ligand, neplanocin A, showed a hydrogen bond-
ing with the active site His301. Surflex-Dock well
reproduced the active conformation of the crystal
ligand. The 50-amino group of compounds 1 and 2
was protonated and used for docking study to simulate
its state in physiological conditions. The protonated 50-
amino group of docked compound 1 appeared to play as
hydrogen bonding donors to active site residues such as
His301, His55, and Asp131. In case of 50-amino-50-deox-
yadenosine (2), the docking study indicated that its pro-
tonated 50-amino group seemed to make smaller number
of hydrogen bonds than 1.
N
X
N
O
HO
OH
a
Compound
IC50 (lM)
1
12.68b
75.02
7.53
2 (X = NH2)
3 (X = NHCONH2)
9 (X = N3)
28.94
a Determined using pure recombinant human placental SAH obtained
from E. coli JM109 containing the plasmid pPROKcd20.
b Data from Ref. 6.
the 50-azido derivative 7 yielded 50-amino derivative 10,
but it was gradually degraded. Thus, compound 10 was
immediately treated with chloroacetyl isocyanate to give
chloroacetyl urea derivative 11. Treatment of 11 with so-
dium methoxide provided the 50-ureido derivative 12
with concomitant removal of the benzoyl group.9,10 Re-
moval of the isopropylidene group in 12 with aqueous
trifluoroacetic acid afforded the final nucleoside 3.8,11
Surflex-Dock of 50-deoxy-50-ureidoadenosine (3) con-
firmed that its 50-ureido group indeed played a role of
multiple hydrogen bonding donor in its binding with
active site residues of SAH as shown in Figure 2. The
multiple hydrogen bondings of the 50-ureido group with
His301 and His55 would contribute to its strong binding
to SAH, and that might cause its potent inhibitory activ-
ity. Compound 9, although its 50-azido group does not
have a hydrogen bonding donor, showed a substantial
level of inhibitory activity. According to the docking
study, it appears to be because an azide nitrogen could
The SAH inhibitory activity of 50-azido-, 50-amino-, and
50-ureido derivatives were measured using pure recombi-
nant human placental SAH obtained from E. coli
JM109 containing the plasmid pPROKcd20, as shown
in Table 1.12
Compounds 2, 3, and 9 were preincubated with the en-
zyme SAH at various concentrations for 5 min at
37 ꢁC and the residual activity of the enzyme was mea-
sured in the synthetic direction toward S-adenosylho-
mocysteine using adenosine and L-homocysteine. As
shown in Table 1, 50-amino-50-deoxyadenosine (2)
exhibited weak enzyme inhibitory activity (IC50
=
75.02 lM), indicating that the 50-amino group is not
enough to form strong hydrogen bonding in the active
site of SAH. However, 50-deoxy-50-ureidoadenosine (3)
showed more potent enzyme inhibitory activity (IC50
7.53 lM) than the 50-amino derivative 1 (IC50
=
=
12.68 lM) or 2 (IC50 = 75.02 lM), indicating that the
50-ureido moiety acted as more powerful and multiple
hydrogen bonding donor than the 50-amino moiety.
Interestingly, the 50-azido derivative 9 showed signifi-
cant enzyme inhibitory activity (IC50 = 28.94 lM) and
better inhibition than the 50-amino derivative 2, al-
though 50-azido group is not a hydrogen bonding donor,
indicating that 50-azido group might form significant
binding in the active site due to its hydrogen bonding
acceptor capability. These findings agreed with the pre-
vious report,13 in which the 50-azido derivative 9 showed
better inhibition of SAH purified from hamster liver
than the 50-amino derivative 2.
Figure 2. Interactions of 50-deoxy-50-ureidoadenosine (3) in the active
site of SAH based on flexible docking. The Surflex-Docked ligand 3 is
displayed in ball-and-stick whose carbon atoms are shown in magenta.
The active site residues are displayed in capped-stick whose carbon
atoms are in white. The non-polar hydrogen atoms are not displayed
for clarity.
In order to examine the binding interactions of the syn-
thesized compounds in the active site, flexible docking

T. Wang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4456–4459
4459
purified by flash silica gel column chromatography
(CH2Cl2/MeOH = 9:1) to give 12 (0.12 g, 58%, three steps)
as a white solid: mp 199.2–202.8 ꢁC; UV (MeOH) kmax
play a hydrogen bonding acceptor with the side-chain
hydroxyl group of Thr157.
18
258.5 nm; ½aꢀD ꢁ103.8; (c 0.50, MeOH); IR (KBr) 3433,
In conclusion, we have accomplished the synthesis of 50-
deoxy-50-ureidoadenosine (3) as a potent SAH inhibitor.
From this study, 50-ureido moiety was discovered as effec-
tive multiple hydrogen bonding donor in the active site of
SAH. We are sure that 50-ureido moiety will be extensively
utilized in designing enzyme inhibitors containing a
hydrogen bonding donor as a pharmacophore feature.
1
1637 cmꢁ1; H NMR (400 MHz, CD3OD) d 8.26 (d, 2H,
J = 6.0 Hz), 6.14 (d, 1H, J = 2.8 Hz), 5.43–5.45 (dd, 1H,
J = 3.2 Hz, 6.4 Hz), 4.98–5.0 (dd, 1H, J = 3.2 Hz,
J = 6.4 Hz), 4.27–4.30 (m, 1H), 3.40–3.43 (m, 2H), 1.59
(s, 3H), 1.37 (s, 3H); 13C NMR (100 MHz, DMSO-d6) d
158.5, 156.1, 152.7, 148.8, 139.8, 119.1, 113.4, 88.8, 84.9,
82.9, 81.6, 41.3, 26.9, 25.2.
11. A solution of compound 12 (0.12 g, 0.34 mmol) in 50%
aqueous trifluoroacetic acid was stirred at room temper-
ature for 1 h. After completion of reaction, the reaction
mixture was evaporated under reduced pressure and co-
evaporated with toluene. The residue was purified on
Dowex 50WX8-200 (H+) resin column to give the final
nucleoside 3 (0.066 g, 63%), which was recrystallized from
Acknowledgments
This work was supported by grants from the Korea
Research Foundation (KRF-2005-005-J01502) and the
National Core Research Center (NCRC) program
(No. R15-2006-020) of the Ministry of Science and
Technology (MOST) and the Korea Science and Engi-
neering Foundation (KOSEF) through the Center for
Cell Signaling & Drug Discovery Research at Ewha Wo-
mans University.
methonal: mp 251.3–252.2ꢁC; UV (MeOH) kmax 285.5 nm;
18
½aꢀD ꢁ27.2 (c 0.18, DMSO); IR (KBr): 3444, 1637 cmꢁ1
;
1H NMR (400 MHz, DMSO-d6) d 8.34 (s, 1H), 8.18 (s,
1H), 7.29 (s, 2H), 6.23 (t, 1H, J = 5.6 Hz,), 5.85 (d, 1H,
J = 6.4 Hz), 5.49 (s, 2H), 5.42 (d, 1H, J = 6.4 Hz), 5.22 (d,
1H, J = 4.4 Hz), 4.63–4.68 (dd, 1H, J = 6.4 Hz, 11.6 Hz),
4.04–4.09 (m, 1H), 3.87–3.91 (m, 1H), 3.35–3.39 (m, 1H),
3.19–3.26 (m, 1H); 13C NMR (100 MHz, DMSO-d6) d
159.3, 156.1, 153.1, 149.7, 140.4, 119.4, 87.6, 84.4, 73.0,
71.3, 41.8. Anal. Calcd for C11H15N7O4: C, 42.72; H, 4.89;
N, 31.70. Found: C, 42.70; H, 4.49; N, 31.41.
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